GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsC in Shewanella amazonensis SB2B

Align IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized)
to candidate 6936959 Sama_1133 PTS system, glucose-specific IIBC component (RefSeq)

Query= TCDB::Q8GBT6
         (403 letters)



>FitnessBrowser__SB2B:6936959
          Length = 485

 Score =  236 bits (601), Expect = 1e-66
 Identities = 137/391 (35%), Positives = 216/391 (55%), Gaps = 23/391 (5%)

Query: 5   QRIGRSLMLPVAVLPAAALLVRLGNADMLGRPEFPAFVTKIAG-FMAAGGNAILDNMALL 63
           QR+ ++L++P+A+LPAA +++ +    +        F+  +A   M + G  I D M +L
Sbjct: 24  QRLSQTLLIPIAILPAAGVMIGIATNPL-------PFIPDVANVLMLSVGKLIFDIMPML 76

Query: 64  FAVGIAIGFAKKSDGSTALAAVVGYLVFKNVLATFTDK-NLPQVAKAVDGKVVMVDAPVD 122
           FA+ +AIGF +   G  A +A  GY V  + LA      +LP         +V     +D
Sbjct: 77  FAIAVAIGFCR-DQGIAAFSAAFGYGVLLSTLAAAAKVYHLPS-------HIVWGTPTID 128

Query: 123 AKVLGGVVMGLVVALLYQRFYRTKLPDWAGFFGGRRLVPILSAFAGLVIGIVFGYIWPVL 182
             + GG+++G +  +  +   + +LP    FF GRR  P++     +++ ++  +IWP L
Sbjct: 129 TGIAGGMLVGGITCVAVRLSEKLRLPAVFSFFEGRRSAPLIMIPLVMLLAVMLAFIWPPL 188

Query: 183 GTGLHNFGEWLV-GSGAVGAGIFGVANRALIPIGMHHLLNSFPWFQAGEY----EGKSGD 237
              +    +W V    A+  G +G+  R L+P+G+HH+ N+  + + G+Y    E   G+
Sbjct: 189 ALSIERLSDWAVYQEPAIAFGFYGMVERLLLPLGLHHIWNAPFYLEVGQYAHDGEIVRGE 248

Query: 238 IARFLAGDPTAGQFMTGFFPIMMFALPAACLAIVHCARPERRKVVGGMMFSLALTSFVTG 297
           +AR+ AGDP+AG    G+  I M+ LPAA LAI  CA   +R  V G+M S A  S++TG
Sbjct: 249 MARYFAGDPSAGNLAGGYL-IKMWGLPAAALAIWRCADRNQRNRVAGVMLSAATASWLTG 307

Query: 298 VTEPIEFTFMFIAPVLYAIHAVLTGVSMALTWALGMKDGFGFSAGAVDFFLNLGIASNPW 357
           VTEPIEF F+F+AP+LY  HA+LTG++ ++   L M     FS G VDF L    +SN  
Sbjct: 308 VTEPIEFAFLFVAPLLYLCHALLTGLAYSIAILLDMHHSVVFSHGLVDFVLLFPQSSNTH 367

Query: 358 GLALVGVCFAALYYVVFRFAITKFNLPTPGR 388
            +  +G     +YY++FR +I  FNL TPGR
Sbjct: 368 WIWFLGPLTFVIYYILFRASILAFNLKTPGR 398


Lambda     K      H
   0.328    0.143    0.441 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 526
Number of extensions: 30
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 403
Length of database: 485
Length adjustment: 32
Effective length of query: 371
Effective length of database: 453
Effective search space:   168063
Effective search space used:   168063
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory